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Package 30/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
bim1.9.0Brian S. YandellLast Changed Date: 2007-04-24 11:31:42 -0700 Last Changed Rev: 24217 | lamb1 | Linux (SUSE 10.1) | x86_64 | ERROR | skipped | |
wellington | Linux (SUSE 9.2) | i686 | ERROR | skipped | ||
churchill | Solaris 2.9 | sparc | [ ERROR ] | skipped | ||
lemming | Windows Server 2003 (32-bit) | x64 | ERROR | skipped | skipped |
Package: bim |
Version: 1.9.0 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build bim |
RetCode: 1 |
Time: 99.3 seconds |
Status: ERROR |
PackageFile: None |
* checking for file 'bim/DESCRIPTION' ... OK * preparing 'bim': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... NO * use '--force' to overwrite the existing 'INDEX' * installing the package to re-build vignettes * Installing *source* package 'bim' ... ** libs gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c INITVALS.c -o INITVALS.o INITVALS.c: In function 'printX': INITVALS.c:166: warning: format '%5.2f' expects type 'double', but argument 3 has type 'int' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c QTL_MOVE.c -o QTL_MOVE.o QTL_MOVE.c: In function 'checkIntegrity': QTL_MOVE.c:157: warning: suggest parentheses around && within || QTL_MOVE.c:160: warning: suggest parentheses around && within || QTL_MOVE.c:170: warning: format '%d' expects type 'int', but argument 4 has type 'double' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c R_mcmc.c -o R_mcmc.o R_mcmc.c: In function 'R_mcmc': R_mcmc.c:45: warning: unused variable 'new_chrom' R_mcmc.c:44: warning: unused variable 'new_lambda' R_mcmc.c: In function 'setupChromosomes': R_mcmc.c:402: warning: 'mystartptr' may be used uninitialized in this function gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c Utilities.c -o Utilities.o Utilities.c: In function 'dvector': Utilities.c:143: warning: unused variable 'ii' Utilities.c: In function 'ivector': Utilities.c:153: warning: unused variable 'ii' Utilities.c: In function 'cvector': Utilities.c:162: warning: unused variable 'ii' Utilities.c: In function 'lvector': Utilities.c:171: warning: unused variable 'ii' Utilities.c: In function 'cmatrix': Utilities.c:181: warning: unused variable 'j' Utilities.c: In function 'imatrix': Utilities.c:201: warning: unused variable 'j' Utilities.c: In function 'matrix': Utilities.c:219: warning: unused variable 'j' Utilities.c: In function 'smatrix': Utilities.c:240: warning: unused variable 'j' Utilities.c: In function 'dmatrix': Utilities.c:356: warning: unused variable 'j' Utilities.c: In function 'get_int': Utilities.c:497: warning: array subscript has type 'char' Utilities.c: In function 'strupr': Utilities.c:862: warning: array subscript has type 'char' Utilities.c: In function 'strlwr': Utilities.c:874: warning: array subscript has type 'char' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c accept_birth.c -o accept_birth.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c birth.c -o birth.o birth.c: In function 'swap_add_dom': birth.c:585: warning: unused variable 'theparams' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c com.c -o com.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c death.c -o death.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c mcmc.c -o mcmc.o mcmc.c: In function 'mcmc': mcmc.c:40: warning: unused variable 'k' mcmc.c: In function 'birth_death': mcmc.c:169: warning: unused variable 'moves' mcmc.c: In function 'outputResults': mcmc.c:434: warning: 'H' may be used uninitialized in this function gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c ranlib.c -o ranlib.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c read_data.c -o read_data.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c update_parms.c -o update_parms.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c update_qtl.c -o update_qtl.o update_qtl.c: In function 'accept_new_lambda': update_qtl.c:386: warning: unused variable 'qtlNum' gcc -std=gnu99 -G -L/usr/local/lib -o bim.so INITVALS.o QTL_MOVE.o R_mcmc.o Utilities.o accept_birth.o birth.o com.o death.o mcmc.o ranlib.o read_data.o update_parms.o update_qtl.o -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading Loading required package: qtl ** help >>> Building/Updating help pages for package 'bim' Formats: text html latex example Bnapus text html latex example bim-internal text html latex bim.effects text html latex example bim.fdr text html latex example bim.model text html latex example bim.qtl text html latex example bmapqtl.options text html latex example fisch text html latex example plot.bim text html latex example plot.bim.diag text html latex example plot.bim.loci text html latex example plot.bim.mcmc text html latex example plot.bim.model text html latex example read.bim text html latex example read.bmapqtl text html latex example run.bmapqtl text html latex example subset.bim text html latex example summary.bim text html latex example vern text html latex example ** building package indices ... * DONE (bim) * creating vignettes ... ERROR Loading required package: qtl Error: processing vignette 'bim.Rnw' failed with diagnostics: chunk 7 Error in subset.cross(cross, chr) : You must specify either chr or ind. Execution halted